scholarly journals SureTypeSCR: R package for rapid quality control and genotyping of SNP arrays from single cells

F1000Research ◽  
2021 ◽  
Vol 10 ◽  
pp. 953
Author(s):  
Ivan Vogel ◽  
Lishan Cai ◽  
Lea Jerman-Plesec ◽  
Eva R. Hoffmann
Keyword(s):  
Whole Genome Amplification ◽  
State Of The Art ◽  
Single Cells ◽  
Genetic Material ◽  
Cost Effective ◽  
R Package ◽  
Nucleotide Polymorphism ◽  
Single Nucleotide ◽  
Effective Technology ◽  
Good Coverage

Genotyping of single cells using single nucleotide polymorphism arrays is a cost-effective technology that provides good coverage and precision, but requires whole genome amplification (WGA) due to the low amount of genetic material. Since WGA introduces noise, we recently developed SureTypeSC, an algorithm to minimize genotyping errors. Here, we present SureTypeSCR, an R package that integrates a state-of-the-art algorithm (SureTypeSC) for noise reduction in single cell genotyping and unites all common parts of genotyping workflow in a single tool. SureTypeSCR is built on top of the tidyverse ecosystem, which facilitates common operations over the data and allows users to create and experiment with the genotyping pipeline. Furthermore, the workflow of SureTypeSCR can also be used for standard genotyping of bulk DNA for batch processing in a single pipeline. SureTypeSCR is avaliable from: https://github.com/Meiomap/SureTypeSCR

scholarly journals Genome-Wide Linkage Mapping for Preharvest Sprouting Resistance in Wheat Using 15K Single-Nucleotide Polymorphism Arrays

2021 ◽  
Vol 12 ◽  
Author(s):  
Lingli Li ◽  
Yingjun Zhang ◽  
Yong Zhang ◽  
Ming Li ◽  
Dengan Xu ◽  
...  
Keyword(s):  
Single Nucleotide Polymorphism ◽  
Linkage Mapping ◽  
Cost Effective ◽  
Wheat Breeding ◽  
Preharvest Sprouting ◽  
Nucleotide Polymorphism ◽  
Single Nucleotide ◽  
Specific Pcr ◽  
Grain Color ◽  
Sprouting Resistance

Preharvest sprouting (PHS) significantly reduces grain yield and quality. Identification of genetic loci for PHS resistance will facilitate breeding sprouting-resistant wheat cultivars. In this study, we constructed a genetic map comprising 1,702 non-redundant markers in a recombinant inbred line (RIL) population derived from cross Yangxiaomai/Zhongyou9507 using the wheat 15K single-nucleotide polymorphism (SNP) assay. Four quantitative trait loci (QTL) for germination index (GI), a major indicator of PHS, were identified, explaining 4.6–18.5% of the phenotypic variances. Resistance alleles of Qphs.caas-3AL, Qphs.caas-3DL, and Qphs.caas-7BL were from Yangxiaomai, and Zhongyou9507 contributed a resistance allele in Qphs.caas-4AL. No epistatic effects were detected among the QTL, and combined resistance alleles significantly increased PHS resistance. Sequencing and linkage mapping showed that Qphs.caas-3AL and Qphs.caas-3DL corresponded to grain color genes Tamyb10-A and Tamyb10-D, respectively, whereas Qphs.caas-4AL and Qphs.caas-7BL were probably new QTL for PHS. We further developed cost-effective, high-throughput kompetitive allele-specific PCR (KASP) markers tightly linked to Qphs.caas-4AL and Qphs.caas-7BL and validated their association with GI in a test panel of cultivars. The resistance alleles at the Qphs.caas-4AL and Qphs.caas-7BL loci were present in 72.2 and 16.5% cultivars, respectively, suggesting that the former might be subjected to positive selection in wheat breeding. The findings provide not only genetic resources for PHS resistance but also breeding tools for marker-assisted selection.

scholarly journals Implementing Large Genomic Single Nucleotide Polymorphism Data Sets in Phylogenetic Network Reconstructions: A Case Study of Particularly Rapid Radiations of Cichlid Fish

2020 ◽  
Vol 69 (5) ◽  
pp. 848-862 ◽  
Author(s):  
Melisa Olave ◽  
Axel Meyer
Keyword(s):  
Single Nucleotide Polymorphism ◽  
Gene Flow ◽  
Genetic Material ◽  
Cichlid Fish ◽  
Phylogenetic Network ◽  
Phylogenetic Networks ◽  
Nucleotide Polymorphism ◽  
Rapid Radiation ◽  
Data Set ◽  
Single Nucleotide

Abstract The Midas cichlids of the Amphilophus citrinellus spp. species complex from Nicaragua (13 species) are an extraordinary example of adaptive and rapid radiation ($<$24,000 years old). These cichlids are a very challenging group to infer its evolutionary history in phylogenetic analyses, due to the apparent prevalence of incomplete lineage sorting (ILS), as well as past and current gene flow. Assuming solely a vertical transfer of genetic material from an ancestral lineage to new lineages is not appropriate in many cases of genes transferred horizontally in nature. Recently developed methods to infer phylogenetic networks under such circumstances might be able to circumvent these problems. These models accommodate not just ILS, but also gene flow, under the multispecies network coalescent (MSNC) model, processes that are at work in young, hybridizing, and/or rapidly diversifying lineages. There are currently only a few programs available that implement MSNC for estimating phylogenetic networks. Here, we present a novel way to incorporate single nucleotide polymorphism (SNP) data into the currently available PhyloNetworks program. Based on simulations, we demonstrate that SNPs can provide enough power to recover the true phylogenetic network. We also show that it can accurately infer the true network more often than other similar SNP-based programs (PhyloNet and HyDe). Moreover, our approach results in a faster algorithm compared to the original pipeline in PhyloNetworks, without losing power. We also applied our new approach to infer the phylogenetic network of Midas cichlid radiation. We implemented the most comprehensive genomic data set to date (RADseq data set of 679 individuals and $>$37K SNPs from 19 ingroup lineages) and present estimated phylogenetic networks for this extremely young and fast-evolving radiation of cichlid fish. We demonstrate that the MSNC is more appropriate than the multispecies coalescent alone for the analysis of this rapid radiation. [Genomics; multispecies network coalescent; phylogenetic networks; phylogenomics; RADseq; SNPs.]

scholarly journals Testing Hardy–Weinberg disequilibrium using the generalized linear model

2012 ◽  
Vol 94 (6) ◽  
pp. 319-330 ◽  
Author(s):  
SHIZHONG XU
Keyword(s):  
Linear Model ◽  
Generalized Linear Model ◽  
Human Gene ◽  
R Package ◽  
Snp Markers ◽  
Nucleotide Polymorphism ◽  
Single Nucleotide ◽  
Exact Test ◽  
Multiple Loci ◽  
Probit Link

SummaryCurrent methods for detecting Hardy–Weinberg disequilibrium (HWD) only deal with one locus at a time. We developed a method that can jointly detect HWD for multiple loci. The method was developed under the generalized linear model (GLM) using the probit link function. When applied to a single locus, the new method is more powerful than the exact test. When applied to two or more loci, the method can reduce false positives caused by linkage disequilibrium (LD). We applied the method to 24 single nucleotide polymorphism (SNP) markers of a single human gene and eliminated several false positive HWDs due to LD. We developed an R package ‘hwdglm’ for joint HWD detection, which can be downloaded from our personal website (www.statgen.ucr.edu).

scholarly journals DiscoSnp-RAD: de novo detection of small variants for RAD-Seq population genomics

PeerJ ◽  
2020 ◽  
Vol 8 ◽  
pp. e9291
Author(s):  
Jérémy Gauthier ◽  
Charlotte Mouden ◽  
Tomasz Suchan ◽  
Nadir Alvarez ◽  
Nils Arrigo ◽  
...  
Keyword(s):  
Evolutionary Biology ◽  
Restriction Site ◽  
Population Genomics ◽  
De Novo ◽  
State Of The Art ◽  
Phylogenetic Reconstruction ◽  
Original Method ◽  
Nucleotide Polymorphism ◽  
Single Nucleotide ◽  
Require Time

Restriction site Associated DNA Sequencing (RAD-Seq) is a technique characterized by the sequencing of specific loci along the genome that is widely employed in the field of evolutionary biology since it allows to exploit variants (mainly Single Nucleotide Polymorphism—SNPs) information from entire populations at a reduced cost. Common RAD dedicated tools, such as STACKS or IPyRAD, are based on all-vs-all read alignments, which require consequent time and computing resources. We present an original method, DiscoSnp-RAD, that avoids this pitfall since variants are detected by exploiting specific parts of the assembly graph built from the reads, hence preventing all-vs-all read alignments. We tested the implementation on simulated datasets of increasing size, up to 1,000 samples, and on real RAD-Seq data from 259 specimens of Chiastocheta flies, morphologically assigned to seven species. All individuals were successfully assigned to their species using both STRUCTURE and Maximum Likelihood phylogenetic reconstruction. Moreover, identified variants succeeded to reveal a within-species genetic structure linked to the geographic distribution. Furthermore, our results show that DiscoSnp-RAD is significantly faster than state-of-the-art tools. The overall results show that DiscoSnp-RAD is suitable to identify variants from RAD-Seq data, it does not require time-consuming parameterization steps and it stands out from other tools due to its completely different principle, making it substantially faster, in particular on large datasets.

scholarly journals Cell fixation and preservation for droplet-based single-cell transcriptomics

2017 ◽  
Author(s):  
Jonathan Alles ◽  
Nikos Karaiskos ◽  
Samantha D. Praktiknjo ◽  
Stefanie Grosswendt ◽  
Philipp Wahle ◽  
...  
Keyword(s):  
Single Cell ◽  
Single Cells ◽  
Transcriptional Profiling ◽  
Cost Effective ◽  
R Package ◽  
Fixation Method ◽  
Recent Developments ◽  
Cell Gene Expression ◽  
Rare Cells ◽  
Cell Fixation

ABSTRACTBackgroundRecent developments in droplet-based microfluidics allow the transcriptional profiling of thousands of individual cells, in a quantitative, highly parallel and cost-effective way. A critical, often limiting step is the preparation of cells in an unperturbed state, not compromised by stress or ageing. Another challenge are rare cells that need to be collected over several days, or samples prepared at different times or locations.ResultsHere, we used chemical fixation to overcome these problems. Methanol fixation allowed us to stabilize and preserve dissociated cells for weeks. By using mixtures of fixed human and mouse cells, we showed that individual transcriptomes could be confidently assigned to one of the two species. Single-cell gene expression from live and fixed samples correlated well with bulk mRNA-seq data. We then applied methanol fixation to transcriptionally profile primary single cells from dissociated complex tissues. Low RNA content cells from Drosophila embryos, as well as mouse hindbrain and cerebellum cells sorted by FACS, were successfully analysed after fixation, storage and single-cell droplet RNA-seq. We were able to identify diverse cell populations, including neuronal subtypes. As an additional resource, we provide ‘dropbead’, an R package for exploratory data analysis, visualization and filtering of Drop-seq data.ConclusionsWe expect that the availability of a simple cell fixation method will open up many new opportunities in diverse biological contexts to analyse transcriptional dynamics at single cell resolution.

scholarly journals Highly Multiplexed Spatial Mapping of Microbial Communities

2019 ◽  
Author(s):  
Hao Shi ◽  
Warren Zipfel ◽  
Ilana Brito ◽  
Iwijn De Vlaminck
Keyword(s):  
Microbial Communities ◽  
Spatial Organization ◽  
Single Cells ◽  
Cost Effective ◽  
Probe Design ◽  
E Coli ◽  
Rich Diversity ◽  
Effective Technology ◽  
Phylogenetic Resolution

ABSTRACTMapping the complex biogeography of microbial communities in situ with high taxonomic and spatial resolution poses a major challenge because of the high density and rich diversity of species in environmental microbiomes and the limitations of optical imaging technology. Here, we introduce High Phylogenetic Resolution microbiome mapping by Fluorescence In-Situ Hybridization (HiPR-FISH), a versatile and cost-effective technology that uses binary encoding and spectral imaging and machine learning based decoding to create micron-scale maps of the locations and identities of hundreds of microbial species in complex communities. We demonstrate the ability of 10-bit HiPR-FISH to distinguish 1023 E. coli strains, each fluorescently labeled with a unique binary barcode. HiPR-FISH, in conjunction with custom algorithms for automated probe design and segmentation of single-cells in the native context of tissues, reveals the intricate spatial architectures formed by bacteria in the human oral plaque microbiome and disruption of spatial networks in the mouse gut microbiome in response to antibiotic treatment. HiPR-FISH provides a framework for analyzing the spatial organization of microbial communities in tissues and the environment at single cell resolution.

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